Apologies up-front for a post that can interest only other Porsche 917 freaks. In its day and in retrospect the 917 became famous for four things: 1) Porsche's first "big league" racing sports car, 2) the audacity and financial risk of building 25 prototypes to turn them into FIA-homologated "production" racers, 3) a very unsuccessful first season, 4) complete dominance when it was finally sorted. The story of 917-003 is a footnote to that lost first season.
Walter Naher's Porsche 917: Archive And Works Catalogue is the botany book when you want to get into the weeds of the 917. Most of the facts in this post come from Naher's book. Chassis 003 had two small aerodynamic tweaks, one unsuccessful and one apparently immaterial, that appeared on no other 917's. (None of the pictures here are from Naher's book, although it has many previously unpublished photos.)
Porsche learned that the original 917 was unstable at racing speeds at the LeMans Test Days in March of 1969. After the Test Days, wind tunnel tests were scheduled, but Porsche couldn't get a date in Stuttgart's wind tunnel until May. The tests validated that the stabilizing fins tried on 003's L body in March were worse than useless. But there was not enough time to design and test aero fixes before LeMans, in June. So the 917 L (but not 003) ran at LeMans as originally designed. (The cars were a handful, and DNF.)
Similarly, the Spa-Francorchamps 1000 Km race in early May did not allow time for validated changes to the K body. Jo Siffert tried 003 (with a short tail) and set a time that would have put him on pole for the race. But he was so skeptical of the car's drivability that he chose a 908 instead. 003's race number was transferred to 024/002, to be driven by Gerhard Mitter and Udo Schutz. Having brought two 917's, Porsche was determined to get some actual racing experience with the car. This did not work out well: 024/002 retired on lap 1 with a broken valve spring. (It probably worked out fine for Mitter and Schutz. ;-) )
The other interesting aero tweak on 003 at Spa was the fairings behind the front wheels and in front of the rear ones. The fairings are clearly visible in the picture below and also if you look closely at the picture above at LeMans (six weeks earlier). These fairings, very similar to those that appeared on the 908/2 "flounder" body in 1970, were used on no other 917 as best as I can discover.
003 was disassembled at the end of June. Some parts were apparently used for the prototype Spyder (027) and chassis 003 was scrapped in December, 1969, after a crash. Naher doesn't explain the crash, so I hypothesize that what was left of 003 was still being used as a test mule after the June disassembly.
After the 917 K's aerodynamics were finally sorted out by the Horsman tail late in 1969, the car also received a new wider, squared-off, nose for 1970. It provided for bigger brake ducts and wider tires. The Horsman tail was faired around the upper sides of the 917's now much wider rear tires. The slippery L body wasn't sorted until the late spring of 1970, after a car with higher upper rear fins was crashed in testing. The solution, which led LeMans for hours in June (but was DNF), was a larger rear wing. After that, the L's bodywork was tinkered but basically unchanged: problem solved.
But, aside from 003's, the lower side pods on all 917's remained the same from beginning to end. Naher does not mention 003's fairings in his remarkably detailed history. We are left to wonder why they were tried at all, only once, and abandoned.